debugging link attributes

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debugging link attributes

Dan Staines
Hi chaps,

I'm currently trying to add some additional link attributes between two
existing marts, and everything _looks_ ok in marteditor but my linked
attributes aren't showing up in martview, so I've almost certainly made
a small but crucial mistake somewhere. There are no error messages
regarding missing pointerDatasets etc. in the output or log from
martview, so can anyone suggest some strategies for debugging this kind
of thing?

Thanks,

Dan.

--
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
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Re: debugging link attributes

Damian Smedley
Hi Dan,

I would walk across the corridor and help you but I am in Australia. Best thing is to use the save option in MartEditor to dump the XML onto your file system and then send me the files produced. Can see if I can spot the problem.

Cheers
Damian


On Thu, Jul 22, 2010 at 11:34 AM, Dan Staines <[hidden email]> wrote:
Hi chaps,

I'm currently trying to add some additional link attributes between two existing marts, and everything _looks_ ok in marteditor but my linked attributes aren't showing up in martview, so I've almost certainly made a small but crucial mistake somewhere. There are no error messages regarding missing pointerDatasets etc. in the output or log from martview, so can anyone suggest some strategies for debugging this kind of thing?

Thanks,

Dan.

--
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/

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Re: debugging link attributes

Leandro Hermida-2
In reply to this post by Dan Staines
Hi Dan,

I find MartEditor to be buggy and finicky and have run into similar issues, what I find is that if you export all of the XML files and have a look at them manually you can find where something might not be consistent.  Also examine all the database meta__* tables in the database to make sure everything is sound as these can also get screwed up.  Sometimes that still doesn't solve the problem and I have to start over where I export all the XML and then delete all the meta__* tables.  Then you restart MartEditor and do Naive configuration and then Upload and replace the existing XML with the ones you saved.

best,
Leandro

On Thu, Jul 22, 2010 at 12:34 PM, Dan Staines <[hidden email]> wrote:
Hi chaps,

I'm currently trying to add some additional link attributes between two existing marts, and everything _looks_ ok in marteditor but my linked attributes aren't showing up in martview, so I've almost certainly made a small but crucial mistake somewhere. There are no error messages regarding missing pointerDatasets etc. in the output or log from martview, so can anyone suggest some strategies for debugging this kind of thing?

Thanks,

Dan.

--
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/